rs5906883

Positions:

• chrX-43667695-A-C
• chrX-43667695-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):​c.73+11281A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.60 (15007 hom., 18965 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765

Genes affected

MAOA (HGNC:6833): (monoamine oxidase A) This gene is one of two neighboring gene family members that encode mitochondrial enzymes which catalyze the oxidative deamination of amines, such as dopamine, norepinephrine, and serotonin. Mutation of this gene results in Brunner syndrome. This gene has also been associated with a variety of other psychiatric disorders, including antisocial behavior. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOA	NM_000240.4	c.73+11281A>C		intron_variant		ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.-327+9726A>C		intron_variant			NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.73+11281A>C		intron_variant		1	NM_000240.4	ENSP00000340684	P1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 66295 AN: 109951 Hom.: 15014 Cov.: 22 AF XY: 0.587 AC XY: 18941 AN XY: 32253

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.695

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.615

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.603 AC: 66302 AN: 110005 Hom.: 15007 Cov.: 22 AF XY: 0.587 AC XY: 18965 AN XY: 32317

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.612

Alfa AF: 0.520 Hom.: 2862

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5906883; hg19: chrX-43526943;